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updating include and exclude files, quickstart materials, and auspice…
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… configs from inclusion of new mammal species and sequences from Antarctica
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lhmoncla committed Apr 2, 2024
1 parent e102b3b commit 018f454
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Showing 19 changed files with 43,742 additions and 41,259 deletions.
31,530 changes: 17,246 additions & 14,284 deletions clade-labeling/h5n1-clades.tsv
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53,118 changes: 26,250 additions & 26,868 deletions clade-labeling/h5nx-clades.tsv
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4 changes: 2 additions & 2 deletions clade-labeling/update-clades.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ def append_new_clades(new_clades, old_clades):

"""run label and reformat the output"""
print("\nrunning LABEL to assign clades to", len(new_strains), "new strains of", subtype)
os.system('flu-amd/./LABEL -D {new_strains_fasta} {label_output} H5v2015'.format(new_strains_fasta=new_strains_fasta, label_output=label_output))
os.system('flu-amd-label-2023-05-05/./LABEL -D {new_strains_fasta} {label_output} H5v2023'.format(new_strains_fasta=new_strains_fasta, label_output=label_output))
os.system('python clade-labeling/check-LABEL-annotations.py --label_output {label_output}_final.txt --output {new_clades_file}'.format(new_clades_file=new_clades_file, label_output=label_output))


Expand All @@ -94,4 +94,4 @@ def append_new_clades(new_clades, old_clades):
"""remove intermediate files. You must also remove the LABEL folder otherwise it will throw an error next time about the
project being in use"""
os.system('rm {label_output}_final.txt {label_output}.zip {new_strains_fasta} {new_clades_file}'.format(new_strains_fasta=new_strains_fasta, label_output=label_output, new_clades_file=new_clades_file))
os.system('rm -r flu-amd/LABEL_RES/test_data/{label_output}'.format(label_output=label_output))
os.system('rm -r flu-amd-label-2023-05-05/LABEL_RES/test_data/{label_output}'.format(label_output=label_output))
4 changes: 2 additions & 2 deletions config/auspice_config_h5n1.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"title": "Real-time tracking of influenza A/H5N1 virus evolution",
"maintainers": [
{"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
{"name": "Louise Moncla", "url": "https://lmoncla.github.io/monclalab/"}
],
"build_url": "https://github.com/nextstrain/avian-flu",
"data_provenance": [
Expand Down Expand Up @@ -47,7 +47,7 @@
},
{
"key": "h5_label_clade",
"title": "LABEL clade",
"title": "Provisional LABEL clade",
"type": "categorical"
},
{
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6 changes: 3 additions & 3 deletions config/auspice_config_h5nx.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"title": "Real-time tracking of influenza A/H5NX virus evolution",
"maintainers": [
{"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
{"name": "Louise Moncla", "url": "https://lmoncla.github.io/monclalab/"}
],
"build_url": "https://github.com/nextstrain/avian-flu",
"data_provenance": [
Expand Down Expand Up @@ -47,7 +47,7 @@
},
{
"key": "h5_label_clade",
"title": "LABEL clade",
"title": "Provisional LABEL clade",
"type": "categorical"
},
{
Expand Down Expand Up @@ -92,7 +92,7 @@
],
"display_defaults": {
"map_triplicate": true,
"color_by": "subtype"
"color_by": "region"
},
"filters": [
"host",
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2 changes: 1 addition & 1 deletion config/auspice_config_h7n9.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"title": "Real-time tracking of influenza A/H7N9 evolution",
"maintainers": [
{"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
{"name": "Louise Moncla", "url": "https://lmoncla.github.io/monclalab/"}
],
"build_url": "https://github.com/nextstrain/avian-flu",
"data_provenance": [
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2 changes: 1 addition & 1 deletion config/auspice_config_h9n2.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"title": "Real-time tracking of influenza A/H9N2 virus evolution",
"maintainers": [
{"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"}
{"name": "Louise Moncla", "url": "https://lmoncla.github.io/monclalab/"}
],
"build_url": "https://github.com/nextstrain/avian-flu",
"data_provenance": [
Expand Down
139 changes: 90 additions & 49 deletions config/colors_h5n1.tsv
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Original file line number Diff line number Diff line change
@@ -1,56 +1,97 @@
region antarctica #213A67
region china #4042C7
region southeast_asia #4274CE
region southeast asia #4274CE
region south_asia #5199B7
region south asia #5199B7
region japan_korea #69B091
region japan korea #69B091
region oceania #88BB6C
region west_asia #ADBD51
region west asia #ADBD51
region africa #CEB541
region europe #E39B39
region south_america #E56C2F
region south america #E56C2F
region north_america #DC2F24
region north america #DC2F24
subtype h5n1 #4274CE
subtype h5n2 #E39B39
subtype h5n3 #4042C7
subtype h5n4 #E56C2F
subtype h5n5 #88BB6C
subtype h5n6 #CEB541
subtype h5n7 #ADBD51
subtype h5n8 #69B091
subtype h5n9 #DC2F24
host avian #4066CF
host environment #77B67F
host nonhuman mammal #CEB541
host human #DC2F24
h5_label_clade 0 #5E1D9D
h5_label_clade 1 #521EA7
h5_label_clade 1-8-9-like #4C24B0
h5_label_clade 1.1 #472DB8
h5_label_clade 1.1-like #4335C0
h5_label_clade 1.1.1 #403EC6
h5_label_clade 1.1.2 #3F48C9
h5_label_clade 2-like #3F53CD
h5_label_clade 2.1.1 #3E5DD0
h5_label_clade 2.1.2 #4066CF
h5_label_clade 2.1.3 #4270CE
h5_label_clade 2.1.3.1 #4379CD
h5_label_clade 2.1.3.2 #4682C9
h5_label_clade 2.1.3.2a #4989C4
h5_label_clade 2.1.3.2b #4C91C0
h5_label_clade 2.1.3.3 #5097BA
h5_label_clade 2.2 #549DB3
h5_label_clade 2.2.1 #58A2AC
h5_label_clade 2.2.1.1 #5CA7A5
h5_label_clade 2.2.1.1a #61AB9D
h5_label_clade 2.2.1.2 #67AE95
h5_label_clade 2.2.2 #6CB28D
h5_label_clade 2.2.2.1 #72B485
h5_label_clade 2.3.1 #78B77D
h5_label_clade 2.3.2 #7FB976
h5_label_clade 2.3.2.1 #85BA6E
h5_label_clade 2.3.2.1a #8CBB68
h5_label_clade 2.3.2.1b #93BD62
h5_label_clade 2.3.2.1c #9BBE5C
h5_label_clade 2.3.3 #A2BE57
h5_label_clade 2.3.4 #A9BD53
h5_label_clade 2.3.4-like #B1BD4E
h5_label_clade 2.3.4.1 #B8BC4B
h5_label_clade 2.3.4.2 #BFBB48
h5_label_clade 2.3.4.3 #C5B945
h5_label_clade 2.3.4.4 #CCB742
h5_label_clade 2.4 #D1B340
h5_label_clade 2.5 #D6AF3E
h5_label_clade 3 #DCAB3D
h5_label_clade 3-like #DFA53B
h5_label_clade 4 #E29E39
h5_label_clade 5 #E49838
h5_label_clade 5-6-like #E68F36
h5_label_clade 6 #E68634
h5_label_clade 7 #E67C33
h5_label_clade 7.1 #E67231
h5_label_clade 7.2 #E4652E
h5_label_clade 8 #E2592C
h5_label_clade 8-9-like #E04D29
h5_label_clade 0 #290F54
h5_label_clade 1 #3D167E
h5_label_clade 1-8-9-like #3D167E
h5_label_clade 1.1 #521EA7
h5_label_clade 1.1-like #521EA7
h5_label_clade 1.1.1 #5E1D9D
h5_label_clade 1.1.2 #4C24B0
h5_label_clade 2-like #4C24B0
h5_label_clade 2.1.1 #472DB8
h5_label_clade 2.1.2 #4335C0
h5_label_clade 2.1.3 #403EC6
h5_label_clade 2.1.3.1 #403EC6
h5_label_clade 2.1.3.2 #3F48C9
h5_label_clade 2.1.3.2a #3F53CD
h5_label_clade 2.1.3.2b #3E5DD0
h5_label_clade 2.1.3.3 #4066CF
h5_label_clade 2.2 #4270CE
h5_label_clade 2.2.1 #4379CD
h5_label_clade 2.2.1.1 #4682C9
h5_label_clade 2.2.1.1a #4989C4
h5_label_clade 2.2.1.2 #4C91C0
h5_label_clade 2.2.2 #5097BA
h5_label_clade 2.2.2.1 #549DB3
h5_label_clade 2.3.1 #58A2AC
h5_label_clade 2.3.2 #5CA7A5
h5_label_clade 2.3.2.1 #61AB9D
h5_label_clade 2.3.2.1a #67AE95
h5_label_clade 2.3.2.1b #6CB28D
h5_label_clade 2.3.2.1c #72B485
h5_label_clade 2.3.2.1c-like #78B77D
h5_label_clade 2.3.2.1d #7FB976
h5_label_clade 2.3.2.1e #85BA6E
h5_label_clade 2.3.2.1f #85BA6E
h5_label_clade 2.3.2.1g #8CBB68
h5_label_clade 2.3.3 #93BD62
h5_label_clade 2.3.4 #93BD62
h5_label_clade 2.3.4-like #9BBE5C
h5_label_clade 2.3.4.1 #A2BE57
h5_label_clade 2.3.4.2 #A9BD53
h5_label_clade 2.3.4.3 #A9BD53
h5_label_clade 2.3.4.4 #B1BD4E
h5_label_clade 2.3.4.4-like #B8BC4B
h5_label_clade 2.3.4.4a #BFBB48
h5_label_clade 2.3.4.4b #C5B945
h5_label_clade 2.3.4.4b #C5B945
h5_label_clade 2.3.4.4c #CCB742
h5_label_clade 2.3.4.4d #D1B340
h5_label_clade 2.3.4.4e #D6AF3E
h5_label_clade 2.3.4.4f #DCAB3D
h5_label_clade 2.3.4.4g #DFA53B
h5_label_clade 2.3.4.4h #E29E39
h5_label_clade 2.4 #E49838
h5_label_clade 2.5 #E68F36
h5_label_clade 3 #E68634
h5_label_clade 3-like #E67C33
h5_label_clade 4 #E67231
h5_label_clade 5 #E4652E
h5_label_clade 5-6-like #E4652E
h5_label_clade 6 #E2592C
h5_label_clade 7 #E04D29
h5_label_clade 7.1 #E04D29
h5_label_clade 7.2 #E04D29
h5_label_clade 8 #E04D29
h5_label_clade 8-9-like #DF4127
h5_label_clade 9 #DF4127
h5_label_clade EA-nonGsGD #DD3425
h5_label_clade Am-nonGsGD #891916
Expand Down
130 changes: 81 additions & 49 deletions config/colors_h5nx.tsv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,20 @@
region antarctica #213A67
region china #4042C7
region southeast_asia #4274CE
region southeast asia #4274CE
region south_asia #5199B7
region south asia #5199B7
region japan_korea #69B091
region japan korea #69B091
region oceania #88BB6C
region west_asia #ADBD51
region west asia #ADBD51
region africa #CEB541
region europe #E39B39
region south_america #E56C2F
region south america #E56C2F
region north_america #DC2F24
region north america #DC2F24
subtype h5n1 #4274CE
subtype h5n2 #E39B39
subtype h5n3 #4042C7
Expand All @@ -11,55 +28,70 @@ host avian #4066CF
host environment #77B67F
host nonhuman mammal #CEB541
host human #DC2F24
h5_label_clade 0 #5E1D9D
h5_label_clade 1 #521EA7
h5_label_clade 1-8-9-like #4C24B0
h5_label_clade 1.1 #472DB8
h5_label_clade 1.1-like #4335C0
h5_label_clade 1.1.1 #403EC6
h5_label_clade 1.1.2 #3F48C9
h5_label_clade 2-like #3F53CD
h5_label_clade 2.1.1 #3E5DD0
h5_label_clade 2.1.2 #4066CF
h5_label_clade 2.1.3 #4270CE
h5_label_clade 2.1.3.1 #4379CD
h5_label_clade 2.1.3.2 #4682C9
h5_label_clade 2.1.3.2a #4989C4
h5_label_clade 2.1.3.2b #4C91C0
h5_label_clade 2.1.3.3 #5097BA
h5_label_clade 2.2 #549DB3
h5_label_clade 2.2.1 #58A2AC
h5_label_clade 2.2.1.1 #5CA7A5
h5_label_clade 2.2.1.1a #61AB9D
h5_label_clade 2.2.1.2 #67AE95
h5_label_clade 2.2.2 #6CB28D
h5_label_clade 2.2.2.1 #72B485
h5_label_clade 2.3.1 #78B77D
h5_label_clade 2.3.2 #7FB976
h5_label_clade 2.3.2.1 #85BA6E
h5_label_clade 2.3.2.1a #8CBB68
h5_label_clade 2.3.2.1b #93BD62
h5_label_clade 2.3.2.1c #9BBE5C
h5_label_clade 2.3.3 #A2BE57
h5_label_clade 2.3.4 #A9BD53
h5_label_clade 2.3.4-like #B1BD4E
h5_label_clade 2.3.4.1 #B8BC4B
h5_label_clade 2.3.4.2 #BFBB48
h5_label_clade 2.3.4.3 #C5B945
h5_label_clade 2.3.4.4 #CCB742
h5_label_clade 2.4 #D1B340
h5_label_clade 2.5 #D6AF3E
h5_label_clade 3 #DCAB3D
h5_label_clade 3-like #DFA53B
h5_label_clade 4 #E29E39
h5_label_clade 5 #E49838
h5_label_clade 5-6-like #E68F36
h5_label_clade 6 #E68634
h5_label_clade 7 #E67C33
h5_label_clade 7.1 #E67231
h5_label_clade 7.2 #E4652E
h5_label_clade 8 #E2592C
h5_label_clade 8-9-like #E04D29
h5_label_clade 0 #290F54
h5_label_clade 1 #3D167E
h5_label_clade 1-8-9-like #3D167E
h5_label_clade 1.1 #521EA7
h5_label_clade 1.1-like #521EA7
h5_label_clade 1.1.1 #5E1D9D
h5_label_clade 1.1.2 #4C24B0
h5_label_clade 2-like #4C24B0
h5_label_clade 2.1.1 #472DB8
h5_label_clade 2.1.2 #4335C0
h5_label_clade 2.1.3 #403EC6
h5_label_clade 2.1.3.1 #403EC6
h5_label_clade 2.1.3.2 #3F48C9
h5_label_clade 2.1.3.2a #3F53CD
h5_label_clade 2.1.3.2b #3E5DD0
h5_label_clade 2.1.3.3 #4066CF
h5_label_clade 2.2 #4270CE
h5_label_clade 2.2.1 #4379CD
h5_label_clade 2.2.1.1 #4682C9
h5_label_clade 2.2.1.1a #4989C4
h5_label_clade 2.2.1.2 #4C91C0
h5_label_clade 2.2.2 #5097BA
h5_label_clade 2.2.2.1 #549DB3
h5_label_clade 2.3.1 #58A2AC
h5_label_clade 2.3.2 #5CA7A5
h5_label_clade 2.3.2.1 #61AB9D
h5_label_clade 2.3.2.1a #67AE95
h5_label_clade 2.3.2.1b #6CB28D
h5_label_clade 2.3.2.1c #72B485
h5_label_clade 2.3.2.1c-like #78B77D
h5_label_clade 2.3.2.1d #7FB976
h5_label_clade 2.3.2.1e #85BA6E
h5_label_clade 2.3.2.1f #85BA6E
h5_label_clade 2.3.2.1g #8CBB68
h5_label_clade 2.3.3 #93BD62
h5_label_clade 2.3.4 #93BD62
h5_label_clade 2.3.4-like #9BBE5C
h5_label_clade 2.3.4.1 #A2BE57
h5_label_clade 2.3.4.2 #A9BD53
h5_label_clade 2.3.4.3 #A9BD53
h5_label_clade 2.3.4.4 #B1BD4E
h5_label_clade 2.3.4.4-like #B8BC4B
h5_label_clade 2.3.4.4a #BFBB48
h5_label_clade 2.3.4.4b #C5B945
h5_label_clade 2.3.4.4b #C5B945
h5_label_clade 2.3.4.4c #CCB742
h5_label_clade 2.3.4.4d #D1B340
h5_label_clade 2.3.4.4e #D6AF3E
h5_label_clade 2.3.4.4f #DCAB3D
h5_label_clade 2.3.4.4g #DFA53B
h5_label_clade 2.3.4.4h #E29E39
h5_label_clade 2.4 #E49838
h5_label_clade 2.5 #E68F36
h5_label_clade 3 #E68634
h5_label_clade 3-like #E67C33
h5_label_clade 4 #E67231
h5_label_clade 5 #E4652E
h5_label_clade 5-6-like #E4652E
h5_label_clade 6 #E2592C
h5_label_clade 7 #E04D29
h5_label_clade 7.1 #E04D29
h5_label_clade 7.2 #E04D29
h5_label_clade 8 #E04D29
h5_label_clade 8-9-like #DF4127
h5_label_clade 9 #DF4127
h5_label_clade EA-nonGsGD #DD3425
h5_label_clade Am-nonGsGD #891916
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27 changes: 27 additions & 0 deletions config/include_strains_h5n1.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,27 @@
A/Colorado/18/2022
A/England/215201407/2021
A/Astrakhan/3212/2020
A/Goose/Guangdong/1/1996
A/Mink/Spain/3691822VIR1058610/2022
A/Mink/Spain/3691222VIR105868/2022
A/Mink/Spain/36911022VIR1058611/2022
A/mink/Spain/22VIR127741438693/2022
A/mink/Spain/22VIR127741338692/2022
A/Mink/Spain/3691322VIR105869/2022
A/Cambodia/NPH230032/2023
A/domesticcat/Poland/Kot1/2023
A/domesticcat/Poland/H254/2023
A/domesticcat/Poland/H252/2023
A/domesticcat/Poland/H249/2023
A/domesticcat/Poland/H253/2023
A/domesticcat/Poland/H248/2023
A/domesticcat/Poland/H247/2023
A/dairycattle/Texas/24008749001original/2024
A/dairycattle/Texas/24008749003original/2024
A/dairycattle/Texas/24008749004original/2024
A/dairycattle/Texas/24008749006original/2024
A/dairycattle/Texas/24008749007original/2024
A/dairycattle/Texas/24008749005original/2024
A/goat/Minnesota/24007234006original/2024
A/goat/Minnesota/24007234009original/2024
A/goat/Minnesota/24007234003original/2024
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